X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=f5a4136f04fc6bf6253c83c52c6c0e3abf8ee919;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=6c8d2df4e20c1d0ae0fe30c8780b6b9595d875ba;hpb=2b4c87aedd62794a540ce318ac80e218bd34480b;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 6c8d2df..f5a4136 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,5 +1,6 @@
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
@@ -19,7 +20,6 @@ import java.net.URL;
 import java.util.Objects;
 import java.util.TreeMap;
 
-
 public class BioJsHTMLOutput
 {
   private AlignmentViewPanel ap;
@@ -53,9 +53,48 @@ public class BioJsHTMLOutput
     {
       String outputFile = getOutputFile();
       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      AlignExportSettingI exportSettings = new AlignExportSettingI()
+      {
+        @Override
+        public boolean isExportHiddenSequences()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportHiddenColumns()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportAnnotations()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportFeatures()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportGroups()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isCancelled()
+        {
+          return false;
+        }
+
+      };
       AlignmentExportData exportData = jalview.gui.AlignFrame
-              .getAlignmentForExport(
-              JSONFile.FILE_DESC, ap.getAlignViewport());
+              .getAlignmentForExport(JSONFile.FILE_DESC,
+                      ap.getAlignViewport(), exportSettings);
       if (exportData.getSettings().isCancelled())
       {
         return;
@@ -68,8 +107,7 @@ public class BioJsHTMLOutput
 
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
+              .replaceAll("#sequenceData#", jalviewAlignmentJson)
               .toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
@@ -91,9 +129,9 @@ public class BioJsHTMLOutput
   {
     String selectedFile = null;
     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "html" }, new String[] { "HTML files" },
+            "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
 
     jvFileChooser.setDialogTitle(MessageManager
@@ -114,9 +152,7 @@ public class BioJsHTMLOutput
     return selectedFile;
   }
 
-
-  public static String getBioJsTemplateAsString()
-          throws IOException
+  public static String getBioJsTemplateAsString() throws IOException
   {
     InputStreamReader isReader = null;
     BufferedReader buffReader = null;
@@ -216,7 +252,6 @@ public class BioJsHTMLOutput
 
   }
 
-
   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
     for (BioJSReleasePojo bjsRelease : repo.getReleases())